Generated using: 20Q1

Overview

Pediatric tumor types with CL data

Pediatric tumor types with CL or tumor data

The plot below all cell lines embedded

Prior to cellinger

The plot below is the output without using cellinger using UMAP

Undifferentiated cluster

Assigned tumor types to cell lines and confidence metrics

Session Info

devtools::session_info()
## ─ Session info ───────────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 3.6.2 (2019-12-12)
##  os       macOS Catalina 10.15.6      
##  system   x86_64, darwin15.6.0        
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       America/New_York            
##  date     2020-09-28                  
## 
## ─ Packages ───────────────────────────────────────────────────────────────────
##  package         * version    date       lib source        
##  AnnotationDbi     1.48.0     2019-10-29 [1] Bioconductor  
##  ape               5.3        2019-03-17 [1] CRAN (R 3.6.0)
##  askpass           1.1        2019-01-13 [1] CRAN (R 3.6.0)
##  assertthat        0.2.1      2019-03-21 [1] CRAN (R 3.6.0)
##  backports         1.1.6      2020-04-05 [1] CRAN (R 3.6.2)
##  bibtex            0.4.2.2    2020-01-02 [1] CRAN (R 3.6.0)
##  Biobase           2.46.0     2019-10-29 [1] Bioconductor  
##  BiocGenerics      0.32.0     2019-10-29 [1] Bioconductor  
##  BiocManager       1.30.10    2019-11-16 [1] CRAN (R 3.6.0)
##  BiocParallel      1.20.1     2019-12-21 [1] Bioconductor  
##  bit               1.1-15.2   2020-02-10 [1] CRAN (R 3.6.0)
##  bit64             0.9-7      2017-05-08 [1] CRAN (R 3.6.0)
##  bitops            1.0-6      2013-08-17 [1] CRAN (R 3.6.0)
##  blob              1.2.1      2020-01-20 [1] CRAN (R 3.6.0)
##  broom             0.5.5      2020-02-29 [1] CRAN (R 3.6.0)
##  callr             3.4.3      2020-03-28 [1] CRAN (R 3.6.2)
##  caTools           1.18.0     2020-01-17 [1] CRAN (R 3.6.0)
##  cellranger        1.1.0      2016-07-27 [1] CRAN (R 3.6.0)
##  cli               2.0.2      2020-02-28 [1] CRAN (R 3.6.0)
##  cluster           2.1.0      2019-06-19 [1] CRAN (R 3.6.2)
##  clusterProfiler * 3.14.3     2020-01-08 [1] Bioconductor  
##  codetools         0.2-16     2018-12-24 [1] CRAN (R 3.6.2)
##  colorspace        1.4-1      2019-03-18 [1] CRAN (R 3.6.0)
##  cowplot           1.0.0      2019-07-11 [1] CRAN (R 3.6.0)
##  crayon            1.3.4      2017-09-16 [1] CRAN (R 3.6.0)
##  crosstalk         1.1.0.1    2020-03-13 [1] CRAN (R 3.6.0)
##  data.table      * 1.12.8     2019-12-09 [1] CRAN (R 3.6.0)
##  DBI               1.1.0      2019-12-15 [1] CRAN (R 3.6.0)
##  dbplyr            1.4.2      2019-06-17 [1] CRAN (R 3.6.0)
##  desc              1.2.0      2018-05-01 [1] CRAN (R 3.6.0)
##  devtools          2.3.0      2020-04-10 [1] CRAN (R 3.6.2)
##  digest            0.6.25     2020-02-23 [1] CRAN (R 3.6.0)
##  DO.db             2.9        2020-02-13 [1] Bioconductor  
##  DOSE              3.12.0     2019-10-29 [1] Bioconductor  
##  dplyr           * 0.8.5      2020-03-07 [1] CRAN (R 3.6.0)
##  DT              * 0.13       2020-03-23 [1] CRAN (R 3.6.0)
##  ellipsis          0.3.0      2019-09-20 [1] CRAN (R 3.6.0)
##  enrichplot        1.6.1      2019-12-16 [1] Bioconductor  
##  europepmc         0.3        2018-04-20 [1] CRAN (R 3.6.0)
##  evaluate          0.14       2019-05-28 [1] CRAN (R 3.6.0)
##  extrafont       * 0.17       2014-12-08 [1] CRAN (R 3.6.0)
##  extrafontdb       1.0        2012-06-11 [1] CRAN (R 3.6.0)
##  fansi             0.4.1      2020-01-08 [1] CRAN (R 3.6.0)
##  farver            2.0.3      2020-01-16 [1] CRAN (R 3.6.0)
##  fastmatch         1.1-0      2017-01-28 [1] CRAN (R 3.6.0)
##  fgsea             1.12.0     2019-10-29 [1] Bioconductor  
##  fitdistrplus      1.0-14     2019-01-23 [1] CRAN (R 3.6.0)
##  forcats         * 0.5.0      2020-03-01 [1] CRAN (R 3.6.0)
##  fs                1.4.1      2020-04-04 [1] CRAN (R 3.6.2)
##  future            1.16.0     2020-01-16 [1] CRAN (R 3.6.0)
##  future.apply      1.4.0      2020-01-07 [1] CRAN (R 3.6.0)
##  gbRd              0.4-11     2012-10-01 [1] CRAN (R 3.6.0)
##  gdata             2.18.0     2017-06-06 [1] CRAN (R 3.6.0)
##  generics          0.0.2      2018-11-29 [1] CRAN (R 3.6.0)
##  ggforce           0.3.1      2019-08-20 [1] CRAN (R 3.6.0)
##  ggplot2         * 3.3.0      2020-03-05 [1] CRAN (R 3.6.0)
##  ggplotify         0.0.5      2020-03-12 [1] CRAN (R 3.6.0)
##  ggpubr          * 0.2.5      2020-02-13 [1] CRAN (R 3.6.0)
##  ggraph            2.0.2      2020-03-17 [1] CRAN (R 3.6.0)
##  ggrepel         * 0.8.2      2020-03-08 [1] CRAN (R 3.6.0)
##  ggridges          0.5.2      2020-01-12 [1] CRAN (R 3.6.0)
##  ggsignif          0.6.0      2019-08-08 [1] CRAN (R 3.6.0)
##  ggthemes        * 4.2.0      2019-05-13 [1] CRAN (R 3.6.0)
##  globals           0.12.5     2019-12-07 [1] CRAN (R 3.6.0)
##  glue              1.4.0      2020-04-03 [1] CRAN (R 3.6.2)
##  GO.db             3.10.0     2020-02-13 [1] Bioconductor  
##  GOSemSim          2.12.1     2020-03-19 [1] Bioconductor  
##  gplots            3.0.3      2020-02-25 [1] CRAN (R 3.6.0)
##  graphlayouts      0.6.0      2020-03-09 [1] CRAN (R 3.6.0)
##  gridExtra       * 2.3        2017-09-09 [1] CRAN (R 3.6.0)
##  gridGraphics      0.5-0      2020-02-25 [1] CRAN (R 3.6.0)
##  gtable            0.3.0      2019-03-25 [1] CRAN (R 3.6.0)
##  gtools            3.8.2      2020-03-31 [1] CRAN (R 3.6.2)
##  haven             2.2.0      2019-11-08 [1] CRAN (R 3.6.0)
##  hms               0.5.3      2020-01-08 [1] CRAN (R 3.6.0)
##  htmltools       * 0.4.0      2019-10-04 [1] CRAN (R 3.6.0)
##  htmlwidgets       1.5.1      2019-10-08 [1] CRAN (R 3.6.0)
##  httr              1.4.1      2019-08-05 [1] CRAN (R 3.6.0)
##  ica               1.0-2      2018-05-24 [1] CRAN (R 3.6.0)
##  igraph            1.2.5      2020-03-19 [1] CRAN (R 3.6.0)
##  IRanges           2.20.2     2020-01-13 [1] Bioconductor  
##  irlba             2.3.3      2019-02-05 [1] CRAN (R 3.6.0)
##  jsonlite          1.6.1      2020-02-02 [1] CRAN (R 3.6.0)
##  KernSmooth        2.23-16    2019-10-15 [1] CRAN (R 3.6.2)
##  knitr             1.28       2020-02-06 [1] CRAN (R 3.6.0)
##  labeling          0.3        2014-08-23 [1] CRAN (R 3.6.0)
##  lattice           0.20-41    2020-04-02 [1] CRAN (R 3.6.2)
##  lazyeval          0.2.2      2019-03-15 [1] CRAN (R 3.6.0)
##  leiden            0.3.3      2020-02-04 [1] CRAN (R 3.6.0)
##  lifecycle         0.2.0      2020-03-06 [1] CRAN (R 3.6.0)
##  limma           * 3.42.2     2020-02-03 [1] Bioconductor  
##  listenv           0.8.0      2019-12-05 [1] CRAN (R 3.6.0)
##  lmtest            0.9-37     2019-04-30 [1] CRAN (R 3.6.0)
##  lsei              1.2-0      2017-10-23 [1] CRAN (R 3.6.0)
##  lubridate         1.7.8      2020-04-06 [1] CRAN (R 3.6.2)
##  magrittr        * 1.5        2014-11-22 [1] CRAN (R 3.6.0)
##  MASS              7.3-51.5   2019-12-20 [1] CRAN (R 3.6.0)
##  Matrix            1.2-18     2019-11-27 [1] CRAN (R 3.6.2)
##  matrixStats     * 0.56.0     2020-03-13 [1] CRAN (R 3.6.0)
##  memoise           1.1.0      2017-04-21 [1] CRAN (R 3.6.0)
##  metap             1.3        2020-01-23 [1] CRAN (R 3.6.0)
##  mnormt            1.5-6      2020-02-03 [1] CRAN (R 3.6.0)
##  modelr            0.1.6      2020-02-22 [1] CRAN (R 3.6.0)
##  multcomp          1.4-13     2020-04-08 [1] CRAN (R 3.6.2)
##  multtest          2.42.0     2019-10-29 [1] Bioconductor  
##  munsell           0.5.0      2018-06-12 [1] CRAN (R 3.6.0)
##  mutoss            0.1-12     2017-12-04 [1] CRAN (R 3.6.0)
##  mvtnorm           1.1-0      2020-02-24 [1] CRAN (R 3.6.0)
##  nlme              3.1-145    2020-03-04 [1] CRAN (R 3.6.0)
##  npsurv            0.4-0      2017-10-14 [1] CRAN (R 3.6.0)
##  numDeriv          2016.8-1.1 2019-06-06 [1] CRAN (R 3.6.0)
##  openssl           1.4.1      2019-07-18 [1] CRAN (R 3.6.0)
##  patchwork         1.0.0      2019-12-01 [1] CRAN (R 3.6.0)
##  pbapply         * 1.4-2      2019-08-31 [1] CRAN (R 3.6.0)
##  pheatmap        * 1.0.12     2019-01-04 [1] CRAN (R 3.6.0)
##  pillar            1.4.3      2019-12-20 [1] CRAN (R 3.6.0)
##  pkgbuild          1.0.6      2019-10-09 [1] CRAN (R 3.6.0)
##  pkgconfig         2.0.3      2019-09-22 [1] CRAN (R 3.6.0)
##  pkgload           1.0.2      2018-10-29 [1] CRAN (R 3.6.0)
##  plotly          * 4.9.2.1    2020-04-04 [1] CRAN (R 3.6.2)
##  plotrix           3.7-7      2019-12-05 [1] CRAN (R 3.6.0)
##  plyr            * 1.8.6      2020-03-03 [1] CRAN (R 3.6.0)
##  png               0.1-7      2013-12-03 [1] CRAN (R 3.6.0)
##  polyclip          1.10-0     2019-03-14 [1] CRAN (R 3.6.0)
##  prettyunits       1.1.1      2020-01-24 [1] CRAN (R 3.6.2)
##  processx          3.4.2      2020-02-09 [1] CRAN (R 3.6.0)
##  progress          1.2.2      2019-05-16 [1] CRAN (R 3.6.0)
##  ps                1.3.2      2020-02-13 [1] CRAN (R 3.6.0)
##  purrr           * 0.3.3      2019-10-18 [1] CRAN (R 3.6.0)
##  qvalue            2.18.0     2019-10-29 [1] Bioconductor  
##  R6                2.4.1      2019-11-12 [1] CRAN (R 3.6.0)
##  RANN              2.6.1      2019-01-08 [1] CRAN (R 3.6.0)
##  RColorBrewer    * 1.1-2      2014-12-07 [1] CRAN (R 3.6.0)
##  Rcpp              1.0.4.6    2020-04-09 [1] CRAN (R 3.6.2)
##  RcppAnnoy         0.0.16     2020-03-08 [1] CRAN (R 3.6.0)
##  Rdpack            0.11-1     2019-12-14 [1] CRAN (R 3.6.0)
##  readr           * 1.3.1      2018-12-21 [1] CRAN (R 3.6.0)
##  readxl          * 1.3.1      2019-03-13 [1] CRAN (R 3.6.0)
##  remotes           2.1.1      2020-02-15 [1] CRAN (R 3.6.0)
##  reprex            0.3.0      2019-05-16 [1] CRAN (R 3.6.0)
##  reshape2          1.4.4      2020-04-09 [1] CRAN (R 3.6.2)
##  reticulate        1.15       2020-04-02 [1] CRAN (R 3.6.2)
##  rlang             0.4.5      2020-03-01 [1] CRAN (R 3.6.0)
##  rmarkdown         2.1        2020-01-20 [1] CRAN (R 3.6.0)
##  ROCR              1.0-7      2015-03-26 [1] CRAN (R 3.6.0)
##  rprojroot         1.3-2      2018-01-03 [1] CRAN (R 3.6.0)
##  RSpectra          0.16-0     2019-12-01 [1] CRAN (R 3.6.0)
##  RSQLite           2.2.0      2020-01-07 [1] CRAN (R 3.6.0)
##  rstudioapi        0.11       2020-02-07 [1] CRAN (R 3.6.0)
##  rsvd              1.0.3      2020-02-17 [1] CRAN (R 3.6.0)
##  Rtsne           * 0.15       2018-11-10 [1] CRAN (R 3.6.0)
##  Rttf2pt1          1.3.8      2020-01-10 [1] CRAN (R 3.6.0)
##  rvcheck           0.1.8      2020-03-01 [1] CRAN (R 3.6.0)
##  rvest             0.3.5      2019-11-08 [1] CRAN (R 3.6.0)
##  S4Vectors         0.24.4     2020-04-09 [1] Bioconductor  
##  sandwich          2.5-1      2019-04-06 [1] CRAN (R 3.6.0)
##  scales          * 1.1.0      2019-11-18 [1] CRAN (R 3.6.0)
##  sctransform       0.2.1      2019-12-17 [1] CRAN (R 3.6.0)
##  sessioninfo       1.1.1      2018-11-05 [1] CRAN (R 3.6.0)
##  Seurat          * 3.1.4      2020-02-26 [1] CRAN (R 3.6.0)
##  sn                1.6-1      2020-04-01 [1] CRAN (R 3.6.2)
##  stringi           1.4.6      2020-02-17 [1] CRAN (R 3.6.0)
##  stringr         * 1.4.0      2019-02-10 [1] CRAN (R 3.6.0)
##  survival          3.1-12     2020-04-10 [1] CRAN (R 3.6.2)
##  testthat          2.3.2      2020-03-02 [1] CRAN (R 3.6.0)
##  TFisher           0.2.0      2018-03-21 [1] CRAN (R 3.6.0)
##  TH.data           1.0-10     2019-01-21 [1] CRAN (R 3.6.0)
##  tibble          * 3.0.0      2020-03-30 [1] CRAN (R 3.6.2)
##  tidygraph         1.1.2      2019-02-18 [1] CRAN (R 3.6.0)
##  tidyr           * 1.0.2      2020-01-24 [1] CRAN (R 3.6.2)
##  tidyselect        1.0.0      2020-01-27 [1] CRAN (R 3.6.2)
##  tidyverse       * 1.3.0      2019-11-21 [1] CRAN (R 3.6.0)
##  triebeard         0.3.0      2016-08-04 [1] CRAN (R 3.6.0)
##  tsne              0.1-3      2016-07-15 [1] CRAN (R 3.6.0)
##  tweenr            1.0.1      2018-12-14 [1] CRAN (R 3.6.0)
##  umap            * 0.2.5.0    2020-03-09 [1] CRAN (R 3.6.0)
##  urltools          1.7.3      2019-04-14 [1] CRAN (R 3.6.0)
##  usethis           1.6.0      2020-04-09 [1] CRAN (R 3.6.2)
##  uwot              0.1.8      2020-03-16 [1] CRAN (R 3.6.0)
##  vctrs             0.2.4      2020-03-10 [1] CRAN (R 3.6.0)
##  viridis           0.5.1      2018-03-29 [1] CRAN (R 3.6.0)
##  viridisLite       0.3.0      2018-02-01 [1] CRAN (R 3.6.0)
##  withr             2.1.2      2018-03-15 [1] CRAN (R 3.6.0)
##  xfun              0.13       2020-04-13 [1] CRAN (R 3.6.2)
##  xml2              1.3.1      2020-04-09 [1] CRAN (R 3.6.2)
##  yaml              2.2.1      2020-02-01 [1] CRAN (R 3.6.0)
##  zoo               1.8-7      2020-01-10 [1] CRAN (R 3.6.0)
## 
## [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library